733a78c585ca10d21d9f7f580eac56d8f9b52584 abenetpa Wed Aug 12 13:47:08 2020 -0700 made new track description page refs #24349 diff --git src/hg/makeDb/trackDb/human/giab.html src/hg/makeDb/trackDb/human/giab.html new file mode 100644 index 0000000..0f0676a --- /dev/null +++ src/hg/makeDb/trackDb/human/giab.html @@ -0,0 +1,81 @@ +<h2>Description</h2> +<p> +The tracks listed here contain data from +<a target="_blank" href="https://www.nist.gov/programs-projects/genome-bottle"><b>The Genome in a Bottle Consortium (GIAB)</b></a>, +an open, public consortium hosted by +<a target="_blank" href="https://www.nist.gov/">NIST</a>. The priority of GIAB is to develop +reference standards, reference methods, and reference data by authoritative characterization of +human genomes for use in <b>benchmarking</b>, including analytical validation and technology +development that will support translation of whole human genome sequencing to clinical practice. The sole +purpose of this work is to provide validated variants and regions to enable technology and +bioinformatics developers to benchmark and optimize their detection methods. + +</p> +<p> +The <b>Ashkenazim and the Chinese Trio tracks</b> show benchmark <b>SNV calls</b> from two +son/father/mother trios of Ashkenazi Jewish and Han Chinese ancestry from the +<a target="_blank" href="https://www.personalgenomes.org/us">Personal Genome Project</a>, +consented for commercial redistribution. +</p> +<p> +The <b>Genome In a Bottle Structural Variants track</b> shows benchmark <b>SV calls</b> (5,262 insertions +and 4,095 deletions, > 50 bp, in 2.51 Gb of the genome) from the son (HG002/NA24385) from the +Ashkenazi Jewish trio. +<p> +</p> +Samples are disseminated as National Institute of Standards and Technology (NIST) +<a target="_blank" href="https://www.coriell.org/1/NIGMS/Collections/NIST-Reference-Materials">Reference Materials</a>. +</p> +<h2>Display Conventions and Configuration</h2> +These tracks are multi-view composite tracks that contain multiple data types (views). Each view +within a track has separate display controls, as described +<a target="_blank" href="https://genome.ucsc.edu/goldenPath/help/multiView.html">here</a>. +</p> +<p> +Unlike a regular genome browser track, the <b>Ashkenazim and the Chinese Trio</b> tracks display +the genome variants of each individual as two <b>haplotypes</b>; SNPs, small insertions and deletions are +mapped to each haplotype based on the <b>phasing</b> information of the VCF file. The <em>haplotype</em> +1 and the <em>haplotype 2</em> are displayed as two separate black lanes for the browser window +region. Each variant is drawn as a vertical dash. <b>Homozygous variants</b> will show two identical +dashes on both haplotype lanes. <b>Phased heterozygous variants</b> are placed on one of the haplotype +lanes and <b>unphased heterozygous variants</b> are displayed in the area between the two haplotype lanes. +</p> +<p> +Predicted de novo variants and variants that are inconsistent with phasing in the trio son can be +colored in <b><font color="red">red</font></b> using the track Configuration options. +</p> + +<h2>Data Access</h2> +The raw data can be explored interactively with the <a target="_blank" href="../cgi-bin/hgTables"> +Table Browser</a>, or the <a target="_blank" href="../cgi-bin/hgIntegrator">Data Integrator</a>. For +automated analysis, the data may be queried from our <a target="_blank" +href="/goldenPath/help/api.html">REST API</a>. +</p> +<p> +Benchmark VCF and BED files for small variants are available for GRCh37 and GRCh38 under each +genome at <a target="_blank" href="ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/">NCBI FTP</a> site. +Structural variants are available for GRCh37 at dbVAR +<a target="_blank" href+"https://www.ncbi.nlm.nih.gov/sites/dbvarapp/studies/nstd175/">nst175</a>. +</p> + +<h2>References</h2> + +<p> +Zook JM, McDaniel J, Olson ND, Wagner J, Parikh H, Heaton H, Irvine SA, Trigg L, Truty R, McLean CY +<em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/30936564" target="_blank"> +An open resource for accurately benchmarking small variant and reference calls</a>. +<em>Nat Biotechnol</em>. 2019 May;37(5):561-566. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/30936564" target="_blank">30936564</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6500473/" target="_blank">PMC6500473</a> +</p> + +<p> +Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, +Boutros PC <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/32541955" target="_blank"> +A robust benchmark for detection of germline large deletions and insertions</a>. +<em>Nat Biotechnol</em>. 2020 Jun 15;. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32541955" target="_blank">32541955</a> +</p> +